fragit.org

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Python peer instruction questions

http://proteinsandwavefunctions.blogspot.com/2015/05/python-peer-instruction-questions.html

Proteins and Wave Functions. Science in the open. Sunday, May 10, 2015. Python peer instruction questions. I am teaching a molecular simulations/intro to python course and have just finished drafting the last sets of peer instruction questions. Here's the last question. The idea is that they have to write a small python program on the spot but this might be more of a take home question. Can you do it? I'm not always this "evil". Here's a more typical one. This work is licensed under a. And here is the li...

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Selecting full residues within a certain distance of another residue or atom in PyMOL

http://proteinsandwavefunctions.blogspot.com/2015/03/selecting-full-residues-within-certain.html

Proteins and Wave Functions. Science in the open. Saturday, March 28, 2015. Selecting full residues within a certain distance of another residue or atom in PyMOL. To select all atoms in a residue (plus any HETATMs) that is within 3 Å of any atom in residue 63 type:. Select br. all within 3 of resi 63. To select all atoms in a residue (plus any HETATMs) that is within 3 Å of the CA atom in residue 63 type:. Select br. all within 3 of 63/CA. If you want to name the selection type. Posted by Jan Jensen.

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: If I deposit a pre-print on arXiv or Nature Precedings where can I submit my paper?

http://proteinsandwavefunctions.blogspot.com/2012/02/if-i-deposit-pre-print-on-arxiv-or.html

Proteins and Wave Functions. Science in the open. Monday, February 27, 2012. If I deposit a pre-print on arXiv or Nature Precedings where can I submit my paper? When we submitted our last paper for publication. We also posted the manuscript on the pre-print server arXiv. This has several advantages:. 1) It makes the work freely accessible to everyone while the paper is being reviewed. 2) It makes the work freely accessible to everyone after its been published. 3) It establishes priority. I wasn't sure ex...

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Bachelor Projects

http://proteinsandwavefunctions.blogspot.com/p/bachelor-projects.html

Proteins and Wave Functions. Science in the open. A predictive model for H/D exchange rates in proteins (7.5 or 15 ECTS). Predicting the CD spectrum of proteins (7.5 or 15 ECTS). Evaluation of fragment based methods and semi-empirical methods of ligand binding in cyclodextrines (7.5 ECTS). Implementation of the pair interaction decomposition analysis in the EFMO method (15 ECTS). Training a Bayesian network using quantum chemical NMR data for fast prediction of protein NMR (7.5 or 15 ECTS). And here is t...

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Planned papers for 2015 - six months in

http://proteinsandwavefunctions.blogspot.com/2015/07/planned-papers-for-2015-six-months-in.html

Proteins and Wave Functions. Science in the open. Friday, July 17, 2015. Planned papers for 2015 - six months in. In January I wrote about the papers I plan to publish. And made this list:. 1 Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal, submitted. 1 Søs Torpenholt, Leonardo De...

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Teaching and Traveling

http://proteinsandwavefunctions.blogspot.com/p/teaching-and-traveling.html

Proteins and Wave Functions. Science in the open. July 22 - Aug 2: Conference vacation. June 27 - July 19: Vacation. Subscribe to: Posts (Atom). News and views on computational chemistry from the Center for Computational Molecular Sciences. At the University of Copenhagen. Blogs by COMS members. R: Plotting multiple categorical data. Frequently, values are plotted against a categorical argument. The categorical argument can be thought of something like a weekday label or a step in a spe. We are trying ou...

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Koding.com: Installing numpy and matplotlib and transferring files

http://proteinsandwavefunctions.blogspot.com/2015/05/kodingcom-installing-numpy-and.html

Proteins and Wave Functions. Science in the open. Saturday, May 2, 2015. Koding.com: Installing numpy and matplotlib and transferring files. Sudo apt-get install python-dev". Sudo pip install numpy" (takes a while). Sudo apt-get install libfreetype6-dev libxft-dev ". Sudo easy install matplotlib ". To transfer files from Koding.com to your computer. Move the file into the web directory (e.g. coordinates end.png). Go to vm setting modal. This work is licensed under a. Creative Commons Attribution 4.0.

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: The main reason I use OA? It makes my research better

http://proteinsandwavefunctions.blogspot.com/2015/04/the-main-reason-i-use-oa-it-makes-my.html

Proteins and Wave Functions. Science in the open. Saturday, April 25, 2015. The main reason I use OA? It makes my research better. Going to hold a talk on #openaccess. In some weeks. Whats the main reason you use #OA. Please RT or MT. Would be cool to show your tweets! Mdash; Steven Ray Wilson (@StevenRayOslo) April 24, 2015. The OA movement has three important "side effects":. 1 Pioneered by PLoS ONE, many OA journals have removed perceived "impact" as a review criterion. I can share our work at any sta...

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Journal of Molecular Modeling considers manuscripts deposited on arXiv

http://proteinsandwavefunctions.blogspot.com/2013/01/journal-of-molecular-modeling-considers.html

Proteins and Wave Functions. Science in the open. Saturday, January 5, 2013. Journal of Molecular Modeling considers manuscripts deposited on arXiv. Thursday, January 03, 2013 2:22 PM. Journal of Molecular Modeling. Re: Manuscript JMMO-D-12-xxx for review. Does JMMO consider paper that have been deposited on the preprint server arXiv? I ask because I am boycotting (i.e. not reviewing for or submitting to) all journals that don't. Best regards, Jan. Sent: Friday, January 04, 2013 9:02 AM. Best regards, Jan.

proteinsandwavefunctions.blogspot.com

Proteins and Wave Functions: Reviews of Casper's second PLoS ONE submission

http://proteinsandwavefunctions.blogspot.com/2012/06/reviews-of-caspers-second-plos-one.html

Proteins and Wave Functions. Science in the open. Wednesday, June 27, 2012. Reviews of Casper's second PLoS ONE submission. The reviews for Casper's second PLoS ONE submission. Submitted around May 25th are in. Let it not be said that all #openaccess papers are carelessly reviewed! I have all but skimmed it but the only major concern of Reviewer #1 is of course very easily dealt with (good point by the way! FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations. When your ...